Variola virus in a 300-year-old Siberian mummy. Philippe Biagini, Catherine Thèves, Patricia Balaresque, Annie Geraut, Catherine Cannet, Christine Keyser, Dariya Nikolaeva, Patrice Gerard, Sylvie Duchesne, Ludovic Orlando, et al.

To cite this version:

Philippe Biagini, Catherine Thèves, Patricia Balaresque, Annie Geraut, Catherine Cannet, et al.. Variola virus in a 300-year-old Siberian mummy.. New England Journal of Medicine, Massachusetts Medical Society, 2012, 367 (21), pp.2057-9. ￿10.1056/NEJMc1208124￿. ￿hal-00967584￿

HAL Id: hal-00967584 https://hal.archives-ouvertes.fr/hal-00967584 Submitted on 29 Mar 2014

HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. correspondence different standards for patients on the basis of their socioeconomic status. Although this is a 1.0 laudable long-term goal, it means that hospitals Bed size DSH percentage with a high proportion of Medicaid patients are 0.8 much more likely to suffer a penalty for exces- sive readmissions than a hospital with a lower 0.6 proportion of Medicaid patients. This is incred- ibly bad social policy, discouraging hospitals 0.4 from admitting Medicaid patients. Objections to 0.2 it are not merely theoretical — the published Hospitals Penalized (%) penalties show the results of this decision. The 0.0 method used also makes it more likely that a 1 2 3 4 large hospital will be hit with a penalty than a Quartile small hospital with the same readmission rate after adjustment for case mix. The data shown Figure 1. Percentage of Hospitals Penalized, in Figure 1 support these arguments. According to Quartile of Bed Size and Disproportionate This issue will grow in importance in the Share Percentage. next 2 years as the maximum allowable penalty Data are from the Centers for Medicare and Medicaid 2,3 increases from 1% of payments to 2% then 3%. Services. DSH denotes disproportionate share. An additional problem with the method is that patients cannot use the results to assess the probability of having a readmission at hospitals the long term care hospital Prospective Payment System and of different sizes or with different dispropor- fiscal year 2013 rates: final rule (http://cms.gov/Medicare/ Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/FY-2013-IPPS tionate share percentages. -Final-Rule-Home-Page-Items/CMS-1588-F-Text-Version.html). J. Graham Atkinson, D.Phil. 2. Idem. FY 2013 IPPS final rule: Hospital Readmissions Reduc- tion Program — supplemental data (http://cms.gov/Medicare/ 1449 44th St., NW Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/FY-2013- Washington, DC IPPS-Final-Rule-Home-Page-Items/FY2013-Final-Rule-Tables.html). [email protected] 3. Idem. FY 2013 final rule date files (http://cms.gov/Medicare/ Disclosure forms provided by the author are available with the Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/FY-2013- full text of this article at NEJM.org IPPS-Final-Rule-Home-Page-Items/FY2013-Final-Rule-Data-Files .html). 1. Centers for Medicare and Medicaid Services. Hospital inpa- tient Prospective Payment Systems for acute care hospitals and DOI: 10.1056/NEJMc1212281

Variola Virus in a 300-Year-Old Siberian Mummy

To the Editor: Smallpox, which is caused by the (termini) regions. Sequence analysis has revealed variola virus of the Poxviridae family and the or- two main clusters: clade 1 includes variants of thopoxvirus genus, is among the most devastat- variola major, and clade 2 includes West Africa ing human diseases. It may have originated and strains and variola minor (alastrim).2 The oldest spread from Egypt, the Near East, or the Indus sequences that have been characterized originate Valley 3000 to 4000 years ago, and historical re- from biologic samples obtained from patients ports indicate epidemics in China as early as the during the past five to six decades. first century A.D. and in Europe during the 6th In 2004, a French and Russian team identi- century. By the mid-18th century, smallpox was a fied several archeological sites in northeastern worldwide endemic disease. It was eradicated af- Siberia (in Sakha Republic [Yakutia], Russian ter vaccination campaigns began more than 200 Federation). Each site consisted of frozen wooden years ago.1 graves buried in the permafrost and dating from Variola DNA is about 186 kbp, with genes the late 17th to early 18th century.3 One of these distributed across conserved (central) or variable graves contained five frozen mummies (Fig. 1A;

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A B

HPXV VACV MPXV Z96 PoxSib 1 Sum70 4 Tanz65 Sarf65 688 Bots72 Ethio72 Jap51 Kor47 Bangla75 633 986 ChinHorn48 Cng70 Pak69 3 Ind64 Syr72 991 BenDH68 Guin69 634 SierL69 5 BrazGar66 1000 Braz66 CPXV GER 706 CMLV M96 2 594 CPXV GRI CPXV FIN 0.01

Figure 1. Grave Containing Five Mummies and Phylogenetic Analysis of Virus Detected in Tissue Samples Obtained from Mummy 2. Panel A shows a funerary wooden chest identified at the “Shamanic Tree I” site in the Churapcha area of Yakutia. The funerary chest was 3.14 m long, 1.10 m wide, and 0.78 m high. Mummy 1 was a male child who was approxi- mately 5 years of age. Mummy 2 was a female adult who was younger than 23 years of age. Mummy 3 was a female adult. Mummy 4 was a male adult who was older than 30 years of age, and mummy 5 was a child who was younger than 4 years of age. Panel B shows a phylogenetic analysis of concatenated Siberian variola B7R/A30L/E9L partial sequences (PoxSib strain). Numbers in the tree are bootstrap values for relatedness obtained after 1000 replications. Maximum likelihood was generated with the use of a Hasegawa–Kishino–Yano model, and node supports were calcu- lated from 1000 bootstrap pseudoreplicates. PoxSib was the strain identified in this study. Other strains have been identified in patients in Guinea in 1969 (Guin69), Sierra Leone in 1969 (SierL69), Benin (formerly Dahomey) in 1968 (BenDH68), Brazil in 1966 (BrazGar66 and Braz66), Syria in 1972 (Syr72), Pakistan in 1969 (Pak69), India in 1964 (Ind64), South Africa in 1965 (102Natal) (Sarf65), Botswana in 1972 (Bots72), Ethiopia in 1972 (Ethio72), Bangladesh in 1975 (Bangla75), Sumatra in 1970 (Sum70), China in 1948 (ChinHorn48), Korea in 1947 (Kor47), Japan in 1951 (Jap51), Tanzania in 1965 (Tanz65), and Congo in 1970 (Cng70). CMLV M96 denotes camelpox virus M96, CPXV FIN cowpox Finland 2000 MAN, CPXV GER cowpox GER91-3, CPXV GRI cowpox GRI-90, HPXV horsepox virus 76, MPXV Z96 monkeypox Zaire-96, and VACV vaccinia virus Copenhagen–derived clone 1990.

and see the Supplementary Appendix, available presence of blood after a possible hemorrhagic with the full text of this letter at NEJM.org). This episode (Fig. S1 in the Supplementary Appen- discovery was very unusual, since burial of dix). On the basis of these observations, the bodies individually was the standard practice in hypothesis of a sudden and lethal infection was Yakutia at that time. Analysis of the grave also considered, one of which was variola infection. suggested that the corpses were buried shortly We confirmed this hypothesis by performing after death.4 successful polymerase-chain-reaction (PCR) ampli- Biologic samples from mummy 2 were ob- fication of three short fragments (B7R/hemag- tained for histologic and molecular investiga- glutinin, A30L/14-kD protein, and E9L/DNA poly- tions. Microscopical examination of pulmonary merase) of the variola genome (PoxSib strain, tissue showed iron inclusions suggestive of the 718 bp of sequence information) (Fig. S2 in the

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Supplementary Appendix). To rule out the persis- Philippe de Micco, M.D., Ph.D. tence of intact viral particles, long-distance PCR Viral Emergence and Co-Evolution Unit analyses (E9L assay, approximately 2 kb) were Marseille, France performed. No positive results were obtained, Bertrand Ludes, M.D., Ph.D. suggesting an extensive fragmentation of the Eric Crubézy, M.D., Ph.D. Molecular Anthropology and Image Synthesis Laboratory viral genome. Phylogenetic analyses confirmed Toulouse, France that PoxSib was variola-related, clustering to- Supported by the French Archaeological Mission in Oriental gether with 18 representative variola human se- Siberia (Ministry of Foreign and European Affairs, France), quences, but distinct from contemporary clades 1 North-Eastern Federal University (Yakutsk, Sakha Republic), and the Human Adaptation program of the French Polar Institute and 2 (Fig. 1B). Bayesian analysis that included Paul Émile Victor. PoxSib extended the origin of smallpox viral Disclosure forms provided by the authors are available with strains as far back as A.D. 120 (geometric mean, the full text of this letter at NEJM.org. A.D. 928). Thus, PoxSib could be a direct pro- 1. Fenner F, Henderson DA, Arita I, Jezek Z, Ladnyi ID. Small- genitor of modern viral strains or a member of pox and its eradication. Geneva: World Health Organization, 1988. an ancient lineage that did not cause outbreaks 2. Lefkowitz EJ, Wang C, Upton C. Poxviruses: past, present in the 20th century. It could be linked to the and future. Virus Res 2006;117:105-18. epidemic of 1714, which was described in stud- 3. Crubézy E, Amory S, Keyser C, et al. Human evolution in Siberia: from frozen bodies to ancient DNA. BMC Evol Biol ies conducted during the 18th century. The dis- 2010;10:25. ease may have been imported to Yakutia during 4. Crubézy E, Alexeev A. Chamane, Kyss, jeune fille des glaces. Russian conquest.5 Paris: Editions Errance, 2007. 5. Zinner EP. Sibir v izvestiakh zapadnoevropeiskikh poutesh- These data show that mummified bodies fro- estvennikov i outchenykh XVIII v. Vostoshno-Sibirskoe Knijnoe zen in the Siberian permafrost are a reservoir of Izdatelstvo Ed, 1968. DNA fragments from ancient pathogens. This DOI: 10.1056/NEJMc1208124 genetic information could provide clues to past Correspondence Copyright © 2012 Massachusetts Medical Society. epidemics. Philippe Biagini, Ph.D. instructions for letters to the editor Viral Emergence and Co-Evolution Unit Marseille, France Letters to the Editor are considered for publication, subject [email protected] to editing and abridgment, provided they do not contain material that has been submitted or published elsewhere. Catherine Thèves, Ph.D. Please note the following: Patricia Balaresque, Ph.D. • Letters in reference to a Journal article must not exceed 175 Molecular Anthropology and Image Synthesis Laboratory words (excluding references) and must be received within Toulouse, France 3 weeks after publication of the article. Annie Géraut, M.D. • Letters not related to a Journal article must not exceed 400 Catherine Cannet, M.Sc. words. Institute of Legal Medicine • A letter can have no more than five references and one figure Strasbourg, France or table. Christine Keyser, Ph.D. • A letter can be signed by no more than three authors. Molecular Anthropology and Image Synthesis Laboratory • Financial associations or other possible conflicts of interest Strasbourg, France must be disclosed. Disclosures will be published with the Dariya Nikolaeva, M.Sc. letters. (For authors of Journal articles who are responding North-Eastern Federal University to letters, we will only publish new relevant relationships Yakutsk, Russian Federation that have developed since publication of the article.) Patrice Gérard, M.Sc. • Include your full mailing address, telephone number, fax Sylvie Duchesne, M.Sc. number, and e-mail address with your letter. • All letters must be submitted at authors.NEJM.org. Molecular Anthropology and Image Synthesis Laboratory Toulouse, France Letters that do not adhere to these instructions will not be Ludovic Orlando, Ph.D. considered. We will notify you when we have made a decision about possible publication. Letters regarding a recent Journal Eske Willerslev, Ph.D. article may be shared with the authors of that article. We are Center for GeoGenetics unable to provide prepublication proofs. Submission of a Copenhagen, Denmark letter constitutes permission for the Massachusetts Medical Anatoly N. Alekseev, Ph.D. Society, its licensees, and its assignees to use it in the Journal’s North-Eastern Federal University various print and electronic publications and in collections, Yakutsk, Russian Federation revisions, and any other form or medium.

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